Check results for 'cRegulome'

using R version 3.6.2 (2019-12-12)
using platform: x86_64-apple-darwin15.6.0 (64-bit)
using session charset: UTF-8
checking for file ‘cRegulome/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘cRegulome’ version ‘0.3.2’
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... NOTE
Packages suggested but not available for checking:
'org.Hs.eg.db', 'clusterProfiler'
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for executable files ... OK
checking for hidden files and directories ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... OK
checking whether package ‘cRegulome’ can be installed ... [6s/6s] OK
checking installed package size ... OK
checking package directory ... OK
checking ‘build’ directory ... OK
checking DESCRIPTION meta-information ... OK
checking top-level files ... OK
checking for left-over files ... OK
checking index information ... OK
checking package subdirectories ... OK
checking R files for non-ASCII characters ... OK
checking R files for syntax errors ... OK
checking whether the package can be loaded ... OK
checking whether the package can be loaded with stated dependencies ... OK
checking whether the package can be unloaded cleanly ... OK
checking whether the namespace can be loaded with stated dependencies ... OK
checking whether the namespace can be unloaded cleanly ... OK
checking loading without being on the library search path ... OK
checking dependencies in R code ... OK
checking S3 generic/method consistency ... OK
checking replacement functions ... OK
checking foreign function calls ... OK
checking R code for possible problems ... [5s/5s] OK
checking Rd files ... OK
checking Rd metadata ... OK
checking Rd cross-references ... OK
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... OK
checking for unstated dependencies in examples ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [7s/7s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [13s/13s] OK
Running ‘testthat.R’ [12s/12s]
checking for unstated dependencies in vignettes ... OK
checking package vignettes in ‘inst/doc’ ... OK
checking running R code from vignettes ... [1s/1s] NONE
‘case_study.Rmd’using ‘UTF-8’... [0s/0s] OK
‘using_cRegulome.Rmd’using ‘UTF-8’... [0s/0s] OK
checking re-building of vignette outputs ... [13s/13s] WARNING
Error(s) in re-building vignettes:
--- re-building ‘case_study.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.0 (2020-02-14 07:10:20 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.23.0 successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, load, save

R.utils v2.9.2 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
    warnings

Attaching package: 'igraph'

The following object is masked from 'package:R.oo':

    hierarchy

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:igraph':

    normalize, path, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Attaching package: 'IRanges'

The following object is masked from 'package:R.oo':

    trim

Quitting from lines 32-41 (case_study.Rmd)
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'org.Hs.eg.db'
--- failed re-building ‘case_study.Rmd’

--- re-building ‘using_cRegulome.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Picking joint bandwidth of 0.0445
--- finished re-building ‘using_cRegulome.Rmd’

SUMMARY: processing the following file failed:
  ‘case_study.Rmd’

Error: Vignette re-building failed.
Execution halted
checking PDF version of manual ... OK
DONE
Status: 1 WARNING, 1 NOTE